Anthro Notes Sept. 27/12
- Nuclear DNA analysis history: RFLP technique developed by Jeffreys in 1988 was implemented
quickly in the UK, US, and Canada. US private (cell mark 1988) and public (FBI 1988) labs developed
DNA divisions. In Canada there were government labs only. This is a key difference in the delivery of
DNA forensics between Canada, UK, and US. The first key trial was in spring 1989 following a voir
dire hearing. It was the R. vs. McNally case. John Wayne from McMaster University, representing the
RCMP lab, reported a match between McNally and samples recovered from a 68-year-old woman.
McNally, upon hearing the random match probability results (1 in several billion), changed his plea
from not-guilty to guilty. The first major trial in Ontario was R. vs. Johnny Terceira in Oct. 1992.
Exonerations based on DNA lead to the innocence project in the US and the association in defence of
the wrongfully convicted in Canada. Labs today would be based on SNPs if things could be restarted
because 19 SNPs can provide a match probability as high as 1 in 10 billion. As of 2008, CODIS
contained over 5 million offender and forensic profiles and had over 45,000 hits.
- History of mitochondrial genome: Since the early 1970s, it was realized that DNA was present in the
mitochondria of human cells. Mitochondria have a clonal mode of inheritance and it was argued that
they evolved as a symbiotic organelle within the eukaryotic cell to produce energy (endo-symbiotic
hypothesis). Following the sequencing breakthrough by Fred Sanger in the 1970s, a Cambridge team
completely sequenced the mitochondrial genome in 1981. Initially called the Anderson sequence, it
was changed to the Cambridge reference sequence (CRS) with a few modifications. It first gained
prominence in evolutionary anthropology studies in the mid-1980s, particularly in terms of a new
hypothesis on the origins of modern homo sapiens. This hypothesis called out of Africa posited that
homo sapiens sapiens (modern humans) evolved from early sapiens between 100 and 200,000 years
ago. The use of mtDNA in ancient DNA research in the 1980s focused on its suitability for ancient
tissues. This paved the way for work in forensics where degraded tissues are encountered (cold
cases, low product). The first mitochondrial DNA forensic cases occurred in the US and UK in the
mid-1990s. The first case in Canada was R. vs. Murrin following a voir dire hearing (1999). The main
issues raised in the voir dire hearing were 1. Contamination, 2. Heteroplasmy, 3. Science still
debated in terms of recombination and paternal inheritance.
- The eukaryotic cell and mitochondria: In the cell DNA is found in the nucleus and the mitochondria.
The mitochondria are responsible for energy production and most of its genes are used for this
function. In each cell there are hundreds to thousands of mitochondria, which means a high copy
number. Within a mitochondrion there are at least two genomes. This plus the fact that there are
many mitochondria per cell, means there is a high copy number per cell. There are lots of targets for
primers when sequencing. This high copy number is a major reason for the use of mitochondrial DNA
in special cases and in ancient DNA research. mtDNA has a helical structure, just like nuclear DNA.
The mitochondrial genome accumulates lots of mutations with age, and this is an important issue in
- Mitochondrial genome: The CRS focused on the light strand of the mtDNA genome. The genome is
composed of 16,569 bases, which is about 0.1% of all human DNA. This is one reason they focused on
sequencing it first instead of the nuclear DNA genome. The genome contains the information for the
synthesis of 13 proteins, 22 tRNAs, and 12 ribosomal RNAs. These coding genes are mostly found on
the heavy strand. The light strand is C/T rich and the heavy strand is G/A rich. The genome has a
circular configuration. It is not a chromosome, but it is often called the 47 chromosome. There aretwo main regions of the genome used in ancient DNA and forensic work 1. D-loop or hypervariable
region containing HV1 and HV2, 2. Coding region. There are two main approaches restriction
enzymes define haplogroups for ethnic studies in the coding region and direct sequencing of HV1 and
- Division of the mtDNA: The human mt genome is divided into coding and non-coding regions. The
non-coding region, also called the displacement or D-loop region, contains two areas that are
characterized by high mutation rates and are referred to as hypervariable regions 1 and 2. HV1
contains bases 16024 to 16365 and HV2 contains bases 73 to 340. When the genome was first
sequenced, the functions of the various components were unknown. It is likely that had the
functional differences between the non-coding (D-loop) and coding (bp 341-16023) regions and the
role of non-coding regions in forensics been known, the mtDNA sequence would have been started at
- Advantages of mtDNA: high copy number/cell, high mutation rate in D-loop (but this rate is slow),
maternal inheritance, no recombination or mixed parentage, easier statistical analysis.
- High copy number: In a cell there is a single nucleus and hundreds to thousands of mitochondria.
Each mitochondrion contains on average at least 2.2 genomes. This high copy number makes it much
easier to obtain results on highly degraded tissues from crime or mass disaster sites. mtDNA was first
used in ancient DNA research for this reason. The nucleus has two copies of each gene per cell,
inherited from both parents. These are unique to individuals. Mitochondria have 1000s of copies per
cell and they are maternally inherited. They are not unique to individuals. mtDNA can be obtained
from hair shafts.
- High mutation rate in hypervariable region: The hypervariable regions have an unusually high
substitution rate, which is good for determining maternal relationships. Though the mutation rate is
high (10x greater than the coding region and the nuclear DNA genome) there is usually only base
change every 33 generatio